A Spatio-Temporal Analysis Framework for Characterizing Radiation-Induced Genomic Instability

Overview

Chronic low-dose ionizing radiation exposure induces genomic instability that manifests as both structural variants and point mutations. Conventional analytical approaches treat these genomic alterations as independent events, preventing identification of mechanistic coupling between chromosomal rearrangements and localized mutagenesis occurring at breakpoint junctions. This analytical limitation is consequential for understanding cancer risk in populations exposed to low-dose radiation through occupational settings, medical imaging, and environmental contamination. The research addresses this gap by developing an integrated analytical framework that combines temporal pattern tracking, breakpoint-proximal mutation enrichment analysis, and systematic testing across structural variant types to characterize coupled genomic dynamics. The framework was applied to whole-genome sequencing data from primary human endothelial cells exposed to chronic low-dose gamma radiation across multiple dose rates and time points.

Methods and approach

The analytical framework integrates three methodological components: temporal pattern tracking to monitor genomic alterations across exposure duration, breakpoint-proximal mutation enrichment analysis to detect localized mutagenesis near structural variant junctions, and systematic testing across all structural variant types to identify type-specific patterns. Primary human umbilical vein endothelial cells were exposed to chronic low-dose gamma radiation at rates ranging from 0.001 to 2 mGy per hour over a three-week period. Whole-genome sequencing data from these exposures were analyzed to quantify spatial relationships between structural variants and point mutations, with particular attention to distance-dependent enrichment patterns. The framework examines mutation enrichment at multiple distance thresholds from breakpoints and categorizes temporal persistence of genomic alterations to distinguish transient from stable events.

Key Findings

Analysis revealed a 7.13-fold enrichment of doublet base substitutions within 10 base pairs of inversion breakpoints, a signal not observed for other structural variant types. This enrichment exhibited sharp distance-dependent decay, reaching approximately 1.9-fold at 100 base pairs, consistent with localized mutagenesis at inversion junctions. Temporal analysis demonstrated divergent persistence patterns: inversions appeared exclusively at single timepoints (100% transient), whereas doublet base substitutions showed greater temporal stability with 9.0% detected at multiple timepoints. The inversion-doublet base substitution events affected 16 high-constraint genes with probability of loss-of-function intolerance scores of 0.9 or higher. These genes function in DNA damage response, signal transduction, and chromatin regulation pathways essential for genomic stability maintenance.

Implications

The framework establishes a generalizable approach for investigating spatial and temporal relationships between structural variants and point mutations, revealing mechanistic coupling invisible to conventional analyses that treat these alterations independently. The specific enrichment of doublet base substitutions at inversion breakpoints suggests distinct repair processes or mutagenic mechanisms operating at these junctions during chronic low-dose radiation exposure. The transient nature of inversions contrasted with more persistent doublet base substitutions indicates differential cellular selection or repair dynamics for these coupled events. Identification of affected high-constraint genes in DNA damage response and chromatin regulation pathways suggests potential routes through which radiation-induced coupled genomic alterations may compromise genomic stability. The framework has applications extending beyond radiation biology to cancer genomics and mechanistic investigations of DNA repair fidelity, particularly for characterizing genomic instability patterns arising from various mutagenic exposures and endogenous processes.